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Special Issue Information

Dear Colleagues,

Plant-associated microorganisms fulfill important functions for plant growth, health as well as quality. While direct plant growth promotion by microbes is based on improved nutrient acquisition and hormonal stimulation, diverse mechanisms are involved in the suppression of plant pathogens, which is often indirectly connected with plant growth. Based on these beneficial plant–microbe interactions, it is possible to develop microbial inoculants for use in agricultural biotechnology. Dependent on their mode of action and effects, these products can be used as biofertilizers, plant strengtheners, phytostimulators, and biopesticides. There is a strong growing market for microbial inoculants worldwide with an annual growth rate of approximately 10%. The use of genomic technologies leads to products with more predictable and consistent effects. The future success of the biological control industry will benefit from interdisciplinary research, e.g., on mass production, formulation, interactions, and signaling with the environment, as well as on innovative business management, product marketing, and education. Altogether, the use of microorganisms and the exploitation of beneficial plant–microbe interactions offer promising and environmentally friendly strategies for conventional and organic agriculture worldwide. In this special issue all studies regarding biocontrol, plant growth and quality promotion are welcome.

Prof. Dr. Gabriele BergDr. Christin ZachowGuest Editors

Submission

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are refereed through a peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Agronomy is an international peer-reviewed Open Access quarterly journal published by MDPI.

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English correction and/or formatting fees of 250 CHF (Swiss Francs) will be charged in certain cases for those articles accepted for publication that require extensive additional formatting and/or English corrections.

Plants have recently been recognized as meta-organisms due to a close symbiotic relationship with their microbiome. Comparable to humans and other eukaryotic hosts, plants also harbor a “second genome” that fulfills important host functions. These advances were driven by both “omics”-technologies guided by

Plants have recently been recognized as meta-organisms due to a close symbiotic relationship with their microbiome. Comparable to humans and other eukaryotic hosts, plants also harbor a “second genome” that fulfills important host functions. These advances were driven by both “omics”-technologies guided by next-generation sequencing and microscopic insights. Additionally, these new results influence applied fields such as biocontrol and stress protection in agriculture, and new tools may impact (i) the detection of new bio-resources for biocontrol and plant growth promotion, (ii) the optimization of fermentation and formulation processes for biologicals, (iii) stabilization of the biocontrol effect under field conditions, and (iv) risk assessment studies for biotechnological applications. Examples are presented and discussed for the fields mentioned above, and next-generation bio-products were found as a sustainable alternative for agriculture.
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In greenhouse and field experiments, a mycelial formulation of the fungus Myrothecium verrucaria (IMI 361690) containing 0.20% Silwet L-77 surfactant exhibited high bioherbicidal efficacy against the problematic weed hemp sesbania. Infection and mortality levels of 100% of hemp sesbania seedlings occurred within 48 h after fungal application in the greenhouse. In rice field tests conducted over a three year period, M. verrucaria at an inoculum concentration of 50 g L−1 (dry mycelium equivalent) controlled 95% of ≤20 cm tall hemp sesbania plants. M. verrucaria also controlled larger plants (≥60 cm tall) using this high inoculum concentration. This level of weed control, as well as rice yields from plots where weeds were effectively controlled, were similar to those which occurred with the herbicide acifluorfen. These results suggest that a mycelial formulation of M. verrucaria has potential as a bioherbicide for controlling hemp sesbania in rice.
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Climate change increases stress levels for crops and affects the economic and environmental aspects of agricultural management systems. The application of stress tolerance-mediating microorganisms is an auspicious strategy for improving crop protection, and as such, we developed a direct selection strategy to obtain

Climate change increases stress levels for crops and affects the economic and environmental aspects of agricultural management systems. The application of stress tolerance-mediating microorganisms is an auspicious strategy for improving crop protection, and as such, we developed a direct selection strategy to obtain cultivable microorganisms from promising bioresources using the bait plants, maize, oilseed rape, sorghum and sugar beet. Alpine mosses, lichens and primrose were selected as bioresources, as each is adapted to adverse environmental conditions. A 10% crop-specific selection was found for bait plant rhizosphere communities using cultivation-independent fingerprints, and their potential role as stress protecting agents (SPA) was evaluated following the cultivation of captured bacteria. In addition to assays identifying phytopathogen antagonism and plant growth promotion capacities, our evaluation included those that test the ability to allocate nutrients. Moreover, we developed new assays to measure tolerance in diverse stress conditions. A score scheme was applied to select SPAs with desired properties, and three Pseudomonas specieswith pronounced antagonistic activity that showed elevated tolerance to desiccation and an improved seed germination rate were subsequently chosen. Screening for environmentally-conditioned and host-adapted microorganisms provides a novel tool for target-oriented exploitation of microbial bioresources for the management of ecofriendly crops facing biotic and abiotic stresses.
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Microorganisms are involved in a network of interactions with plants, promoting growth and acting as biocontrol agents against diseases. In this work, we studied native microorganisms associated with quinoa plants (Chenopodium quinoa) and the application of these organisms to the organic

Microorganisms are involved in a network of interactions with plants, promoting growth and acting as biocontrol agents against diseases. In this work, we studied native microorganisms associated with quinoa plants (Chenopodium quinoa) and the application of these organisms to the organic production of quinoa in the Andean Altiplano. Quinoa is a non-cereal grain native to the Andean highlands and is highly nutritious and gluten-free. As such, the international demand for quinoa has increased substantially in recent years. We isolated native endophytic bacteria that are able to fix nitrogen, solubilize phosphate and synthesize a phytohormone and native strains of Trichoderma, a fungus typically used for increasing plant growth and tolerance to biotic and abiotic stresses. Greenhouse assays and field trials allowed for selecting promissory bacterial isolates, mostly belonging to Bacillus and Paenibacillus genera, that increased plant length, panicle weight and grain yield. Selected microbial isolates were large-scale multiplied in simple and inexpensive culture media and then formulated to obtain bioproducts that were distributed among local farmers. Thus, we developed a technology for the exploitation of beneficial microbes, offering promising and environmentally friendly strategies for the organic production of quinoa without perturbing the native microbial diversity of Andean soils and making them more resilient to the adverse effects of climatic change and the over-production of quinoa.
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Currently, there is little knowledge of the establishment of repeatedly applied biological control agents (BCAs) in the phyllosphere of plants and, in particular, their interactions with the resident microbiome. Under field conditions, the BCA Aureobasidium pullulans was applied as a model organism to

Currently, there is little knowledge of the establishment of repeatedly applied biological control agents (BCAs) in the phyllosphere of plants and, in particular, their interactions with the resident microbiome. Under field conditions, the BCA Aureobasidium pullulans was applied as a model organism to organically grown strawberries during two subsequent years (2011, 2012), either as single strain treatment or with the co-application of the entomopathogenic fungus Beauveria bassiana. Fungal and bacterial communities of strawberry leaves were investigated by means of plate counts and 454 pyrosequencing. The establishment of the introduced A. pullulans strains considerably differed between the two years, presumably due to distinct environmental conditions. Short-term and long-term effects of BCA applications on the composition and diversity of fungal communities could be observed as a result of successful establishment of A. pullulans, in 2011, showing, for instance, reduced diversity of fungal communities by competitive displacement shortly after BCA introduction. Due to considerable dynamics in untreated resident microbial communities in the phyllosphere in general, however, we suggest that even the effects caused by the applied BCA preparations in 2011 are negligible under practical conditions.
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Monilinia laxa is the causal agent of brown rot disease on stone fruits, and also causes blossom wilt and twig canker. The common practice used to manage this disease is through fungicide treatments. However the demand to reduce fungicide inputs has been increasing

Monilinia laxa is the causal agent of brown rot disease on stone fruits, and also causes blossom wilt and twig canker. The common practice used to manage this disease is through fungicide treatments. However the demand to reduce fungicide inputs has been increasing and there is a growing number of reports of M. laxa strains that are resistant to fungicides. There is an urgent need to search for an alternative strategy to control the disease. This study focused on the isolation and characterisation of biological control agents (BCAs) using indigenous isolates isolated from cherries and plums collected within the UK. A total of 192 isolates were screened against two strains of M. laxa in a series ofin vitro dual culture tests. From this in vitro screen, 12 isolates were selected for a subsequent in vivo screen on detached fruits, which then narrowed these isolates down to two potential BCAs. These two strains were identified as Bacillusamyloliquefaciens/subtilis (isolate B91) and Aureobasidium pullulans (isolate Y126). The capability of these two potential BCAs to grow and survive at a range of temperatures likely to be experienced under field and storage conditions was studied in order to gain knowledge for product formulation and field application. Bacillus sp. B91 was shown to be a mesophilic bacterium that could grow at 10–25 °C but suffered significant mortality at 0 and 5 °C, while A. pullulans Y126 was both mesophilic and psychrotolerant as it grew between 0–25 °C with the optimum at 20 °C. When all nutrients were removed, Y126 was able to survive for several weeks in all test temperatures (0–25 °C) but showed significant mortality at 25 °C. The capability of B91 to survive at 20 and 25 °C was higher than at low temperatures (0–15 °C). In addition, the modes of action of the potential BCAs were studied. B91 was shown to produce soluble and volatile organic compounds that inhibited M. laxa, while A. pullulans Y126 did not produce inhibitory compounds, but appeared to inhibit the pathogen via competition for nutrients. This study shows that microbial antagonists against M. laxa can be found from indigenous sources and that they are capable of preventing brown rot disease in controlled conditions, thus demonstrating a potential to be developed into commercial products.
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To shed light on phytobeneficial bacterial gene expression in situ, we investigated the expression of phlD gene involved in 2,4-diacetylphloroglucinol production. For that purpose, stable isotope probing (SIP) of DNA and mRNA approaches were used. Arabidopsis thaliana seedlings were grown under 13

To shed light on phytobeneficial bacterial gene expression in situ, we investigated the expression of phlD gene involved in 2,4-diacetylphloroglucinol production. For that purpose, stable isotope probing (SIP) of DNA and mRNA approaches were used. Arabidopsis thaliana seedlings were grown under 13CO2 for 27 days, and the presence and expression of phlD gene was determined in the rhizosphere soil and on the roots of A. thaliana. Results showed that phlD was present and expressed by bacteria inhabiting rhizosphere soil and deriving nutrients from the breakdown of organic matter and from root exudates, whereas phlD gene expression seemed to be repressed on roots. These data were validated in vitro by inoculating four plant species by the phytobeneficial bacterium Pseudomonas brassicacearum. phlD gene expression was highly activated by root exudates of wheat and that of Medicago truncatula and to a lesser extent by that of Brassica napus while it was completely suppressed by root exudates of A. thaliana. Overall, these results lead us to the conclusion that the signals to down regulate phl gene expression may derive from A. thaliana root exudates.
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The effectiveness of biological control agent, Ulocladium atrum (isolates U13 and U16)in protecting Vitis vinifera L. cv. Chardonnay against gray mold disease caused by Botrytis cinerea, and simulation of the foliar defense responses was investigated. A degraded mycelium structure during cultural assay on potato dextrose agar revealed that U. atrum isolates U13 and U16 were both antagonistic to B. cinerea, mainly when isolates were inoculated two days before Botrytis. Under in vitro conditions, foliar application of U. atrum protected grapevine leavesagainst gray mold disease. An increase in chitinase activity was induced by the presence of U. atrum isolates indicating that the biological control agentstriggered plant defense mechanisms. Moreover, U13 has the potential to colonize the grapevine plantlets and to improve their growth. The ability of U. atrum isolates to exhibit an antagonistic effect against B. cinerea in addition to their aptitude to induce plant resistance and to promote grapevine growth may explain a part of their biological activity. Hence, this study suggests that U. atrum provides a suitable biocontrol agent against gray mold in grapevines.
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Verticilliumwilt, caused by Verticillium nonalfalfae and V. dahliae, is a devastating disease in hops that can cause considerable economic crop losses. The perennial use of hops combined with the long persistence of the pathogen in soil make it difficult to suppress

Verticilliumwilt, caused by Verticillium nonalfalfae and V. dahliae, is a devastating disease in hops that can cause considerable economic crop losses. The perennial use of hops combined with the long persistence of the pathogen in soil make it difficult to suppress the disease with conventional measures. Biological control agents (BCA) are the basis of an environmentally friendly plant protection strategy that uses plant promotion and antagonistic effects of microorganisms. We evaluated the effect of four selected beneficial bacterial strains, Burkholderia terricola ZR2-12, Pseudomonas poae RE*1-1-14, Serratia plymuthica 3Re4-18, and Stenotrophomonas rhizophila DSM14405T for their use in hops. All strains were shown to be both rhizosphere and endorhiza competent, and their abundances ranged from log10 3.0 to log10 6.2 CFU g−1 root fresh weight in the endorhiza and from log10 2.9 to log10 4.7 CFU g−1 root fresh weight in the rhizosphere with B. terricola ZR2-12 showing the highest overall cell densities. Microscopic visualization of DsRed-labeled transformants with confocal laser scanning microscopy showed different colonization patterns and confirmed the rhizosphere competence. Growth promoting effects on seedlings treated with bacteria were found for S. plymuthica 3Re4-18 and S. rhizophila DSM14405T. Competent colonization and plant growth promoting effects are the most important prerequisites towards efficient biocontrol.
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Two strains, 30N-5 and 30VD-1, identified as Bacillus simplex and B. subtilis, were isolated from the rhizospheres of two different plants, a Podocarpus and a palm, respectively, growing in the University of California, Los Angeles (UCLA) Mildred E. Mathias Botanical Garden. B.

Two strains, 30N-5 and 30VD-1, identified as Bacillus simplex and B. subtilis, were isolated from the rhizospheres of two different plants, a Podocarpus and a palm, respectively, growing in the University of California, Los Angeles (UCLA) Mildred E. Mathias Botanical Garden. B. subtilis is a well-known plant-growth promoting bacterial species, but B. simplex is not. B. simplex 30N-5 was initially isolated on a nitrogen-free medium, but no evidence for nitrogen fixation was found. Nevertheless, pea plants inoculated with B. simplex showed a change in root architecture due to the emergence of more lateral roots. When Pisum sativum carrying a DR5::GUSA construct, an indicator for auxin response, was inoculated with either B. simplex 30N-5 or its symbiont Rhizobium leguminosarum bv. viciae 128C53, GUS expression in the roots was increased over the uninoculated controls. Moreover, when pea roots were coinoculated with either B. simplex 30N-5 or B. subtilis 30VD-1 and R. leguminosarum bv. viciae 128C53, the nodules were larger, clustered, and developed more highly branched vascular bundles. Besides producing siderophores and solubilizing phosphate, the two Bacillus spp., especially strain 30VD-1, exhibited anti-fungal activity towards Fusarium. Our data show that combining nodulating, nitrogen-fixing rhizobia with growth-promoting bacteria enhances plant development and strongly supports a coinoculation strategy to improve nitrogen fixation, increase biomass, and establish greater resistance to fungal disease.
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Inoculation of forest seedlings with mycorrhizal fungi and rhizobacteria can improve the morphological and physiological qualities of plants, especially those used for regeneration of arid areas. In this paper, under standard nursery conditions, Aleppo pine seedlings were inoculated with Pseudomonas fluorescens CECT 5281

Inoculation of forest seedlings with mycorrhizal fungi and rhizobacteria can improve the morphological and physiological qualities of plants, especially those used for regeneration of arid areas. In this paper, under standard nursery conditions, Aleppo pine seedlings were inoculated with Pseudomonas fluorescens CECT 5281 rhizobacteria. Some of these seedlings were also inoculated with the ectomycorrhizal fungus Pisolithus tinctorius. Five months after the inoculations, we examined the growth, water parameters (osmotic potential at full turgor [Ψπfull], osmotic potential at zero turgor [Ψπ0], and the tissue modulus of elasticity near full turgor [Emax]), mycorrhizal colonisation, and concentration of macronutrients (N, P, K, Ca and Mg) in the seedlings. Subsequently, a trial was conducted to assess the root growth potential. P. fluorescens CECT 5281 decreased the cellular osmotic potential of P. halepensis seedlings but increased its elasticity. P. tinctorius + P. fluorescens caused osmotic adjustment at zero turgor and increased tissue elasticity, which improved tolerance to water stress. All inoculations improved the growth and nutrition of the seedlings but caused non-significant effects on root growth potential. The co-inoculation Pisolithus tinctorius + Pseudomonas fluorescens at the nursery may be a suitable technique for producing improved seedling material for restoration purposes.
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Rhodococcuserythropolis is an environmental Gram-positive Actinobacterium with a versatile metabolism involved in various bioconversions and degradations. Rhodococci are best known for their great potential in numerous decontamination and industrial processes. However, they can also prevent plant disease by disrupting quorum sensing-based communication

Rhodococcuserythropolis is an environmental Gram-positive Actinobacterium with a versatile metabolism involved in various bioconversions and degradations. Rhodococci are best known for their great potential in numerous decontamination and industrial processes. However, they can also prevent plant disease by disrupting quorum sensing-based communication of Gram-negative soft-rot bacteria, by degrading N-acyl-homoserine lactone signaling molecules. Such biocontrol activity results partly from the action of the γ-lactone catabolic pathway. This pathway is responsible for cleaving the lactone bond of a wide range of compounds comprising a γ-butyrolactone ring coupled to an alkyl or acyl chain. The aliphatic products of this hydrolysis are then activated and enter fatty acid metabolism. This short pathway is controlled by the presence of the γ-lactone, presumably sensed by a TetR-like transcriptional regulator, rather than the presence of the pathogen or the plant-host in the environment of the Rhodococci. Both the density and biocontrol activity ofR.erythropolis may be boosted in crop systems. Treatment with a cheap γ-lactone stimulator, for example, the food flavoring γ-caprolactone, induces the activity in the biocontrol agent, R. erythropolis, of the pathway degrading signaling molecules; such treatments thus promote plant protection.
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In recent decades, a greater knowledge of chitin chemistry, and the increased availability of chitin-containing waste materials from the seafood industry, have led to the testing and development of chitin-containing products for a wide variety of applications in the agriculture industry. A number

In recent decades, a greater knowledge of chitin chemistry, and the increased availability of chitin-containing waste materials from the seafood industry, have led to the testing and development of chitin-containing products for a wide variety of applications in the agriculture industry. A number of modes of action have been proposed for how chitin and its derivatives can improve crop yield. In addition to direct effects on plant nutrition and plant growth stimulation, chitin-derived products have also been shown to be toxic to plant pests and pathogens, induce plant defenses and stimulate the growth and activity of beneficial microbes. A repeating theme of the published studies is that chitin-based treatments augment and amplify the action of beneficial chitinolytic microbes. This article reviews the evidence for claims that chitin-based products can improve crop yields and the current understanding of the modes of action with a focus on plant-microbe interactions.
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